[Rdkit-discuss] Anaconda build of rdkit: error

Hi all, while trying to install rdkit as part of the Anacond distribution, I get the following error: conda build rdkit [ … messages skipped …] == git describe --tags --dirty == Release_2014_09_1 == git status == HEAD detached at Release_2014_09_1 nothing to commit, working directory

Re: [Rdkit-discuss] libc++ fix for RDKit_2013_06_1

Hi all, all errors are gone with the given changes applied :-) Just for your information, my installation workflow was the following: 1) brew install boost 2) brew install cmake 3) export RDBASE=/usr/local/src/RDKit_2013_09_1 4) Modification of the $RDBASE/Code/RDGeneral/Dict.h file as

Re: [Rdkit-discuss] looking for suggestions: github vs bitbucket vs google code

Hi Greg, I am using bitbucket for my personal projects and it is doing this perfectly fine. However, i keep these private so i have no experience with the public interface. Cheers, Hans On 01 Feb 2013, at 09:54, Greg Landrum greg.land...@gmail.com wrote: I think it's time to move the

Re: [Rdkit-discuss] neutralize charges

Dear all, Andrew and Paul, I have created a short Wiki page with example code at http://code.google.com/p/rdkit/wiki/NeutralisingCompounds I hope it is useful. Hans - www.silicos-it.com A division of Imacosi bvba De Roskam 35, 2970 Schilde Belgium On 12 Oct 2012, at 08:09,

[Rdkit-discuss] Location of C++ UFFOptimizeMolecule() function?

Hi all, according the manual, the C++ signature of the Python function: UFFOptimizeMolecule() should be: int UFFOptimizeMolecule(RDKit::ROMol {lvalue} [,int=200 [,double=10.0 [,int=-1 [,bool=True) However, I cannot find the header file of this function anywhere in the 2012.03.1

[Rdkit-discuss] RDKit / Postgresql installation

Hi, after struggling for some time to get the postgresql extension to RDKit compiled, I now get another error whilst checking the installation: echo $RDBASE /usr/local/src/RDKit_2011_12_1 cd $RDBASE/Code/PgSQL/rdkit make installcheck

Re: [Rdkit-discuss] RDKit / Postgresql installation

Did you by any chance forget to do a make install before the make installcheck? No, both make make install ran fine. 'make install' copied the files as follows: /bin/sh /usr/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -d '/usr/lib/postgresql' /bin/sh

Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)

Hi Gregory (long time since we met)! Why did you use your own 11 smarts for hydrogen bond acceptors instead of rdkit's CalcNumHBA or NumHAcceptors ($([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),$([nH0,o,s;+0]))? The reason why I used a different

Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)

Gregory -the update QED is online.Thx for the contribution.- Hans www.silicos-it.comA division of Imacosi bvbaDe Roskam 35,2970 SchildeBelgium On 04 Apr 2012, at 16:07, Gerebtzoff, Gregori wrote:Hi -A RDKit-based implementation of the QED measure as described by Richard Bickerton (Nature

Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)

there was no "__init__.py" file in "silicos_it" folder.So, import was failed.Do you have any idea? Thanks.2012年3月30日23:27 Hans De Winter h...@silicos-it.com: Hi -A RDKit-based implementation of the QED measure as described by Richard Bickerton (Nature Chemistry, 2012, 4, 90-98)

[Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)

Hi -A RDKit-based implementation of the QED measure as described by Richard Bickerton (Nature Chemistry, 2012, 4, 90-98) has been implemented and made available for download from our website ( www.silicos-it.com Biscu-it).Regards,- Hans www.silicos-it.comA division of Imacosi bvbaDe Roskam

Re: [Rdkit-discuss] improving substructure search behavior with real molecules

Here's a less obvious one:| OCO | [CH] | Yes |I would argue that this one is correct because "C[H]" is asubstructure of "OC([H])([H])O"I always thought that by not specifying a 'count', it defaults to a count of 1 (~ the SMARTS manual at the Daylight site:

[Rdkit-discuss] Minor bug in Data/BaseFeatures.fdef

RDKit 2011-09:on line 31 of Data/BaseFeatures.fdef it says 'Atomtype ChalcAcceptor [o;+0]' while the description in the line above says '# Removed aromatic sulfur from ChalcAcceptor definition'. As such I guess line 31 should read:'Atomtype ChalcAcceptor [s;+0]'?Regards,Hans Silicos-IT is a

[Rdkit-discuss] Pointing to an example of how to use the reaction stuff (in C++ rdkit)

Dear all, I browsed the rdkit-discuss mail archives but couldn't find anything helpful. I just wanted to have a couple of lines of example code (written in C++, not python!) on how to transform a protonated -COOH group into a deprotonated one -COO[-]. I experimented with the

Re: [Rdkit-discuss] Linking RDKit libraries to C++ code

Hi, I've succesfully managed to compile/link/run the following code (Thx to Greg and Eddie): --- #include GraphMol/FileParsers/MolSupplier.h int main(int argc, char *argv[]) { RDKit::SmilesMolSupplier supplier(/Users/hans/Silicos-it/Databases/eMolecules/02-eMolecules-2011-01-02.smi,